As far as I know, AKAIO fully supports the 3-in-1.
I'm not sure exactly what that means, but I would guess that you can run the GBA game from the AceKard and it will copy it to the 3-in-1 and run.
If not, you can always use GBAExploader to run the game.

Put the 3in1 in the DS. Select your GBA game. AKAIO will load the GBA game (and save) to the 3in1 and off you go. Next time you turn on the GBA with the 3in1 in it, AKAIO will back up your save.

twiztidsinz is right about GBA ExpLoader; you can use it to run games. The bad thing about it is that you need to manually handle the save files. The nice thing about GBA ExpLoader is that you can make the 3in1 into a "real" cartridge (i.e. copy your retail Pokemon FireRed to the 3in1 and migrate into D/P/Pl).